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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GraBCas Resource Report Resource Website |
GraBCas (RRID:SCR_000205) | GraBCas | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites. | matlab, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:15980455 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01674, biotools:grabcas | https://bio.tools/grabcas | SCR_000205 | 2026-09-05 06:24:16 | 0 | ||||||
|
GPS-Calpain Cleavage Detector Resource Report Resource Website 1+ mentions |
GPS-Calpain Cleavage Detector (RRID:SCR_000202) | GPS-CCD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites. | calpain, cleavage detector, prediction | is listed by: OMICtools | PMID:21533053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01673 | SCR_000202 | Calpain Cleavage Detector | 2026-09-05 06:24:14 | 4 | ||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-09-05 06:24:17 | 2 | |||||||
|
ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-09-05 06:24:17 | 3 | |||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-09-05 06:24:17 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | 2026-09-05 06:24:19 | 2 | ||||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | 2026-09-05 06:24:17 | 0 | |||||||||
|
ABrowse Resource Report Resource Website 1+ mentions |
ABrowse (RRID:SCR_000345) | software resource | A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks. | genome browser, collaborative work, open data access, collaborative work support, framework, import annotation |
is listed by: OMICtools is related to: Galaxy |
PMID:22222089 | Free, Available for download, Freely available | OMICS_00899 | SCR_000345 | 2026-09-05 06:24:17 | 4 | ||||||||
|
GPViz Resource Report Resource Website |
GPViz (RRID:SCR_000346) | GPViz | software resource | A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. | gene, visualization, genomic, variant, bioinformatics, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00915 | SCR_000346 | 2026-09-05 06:24:19 | 0 | ||||||||
|
iASeq Resource Report Resource Website |
iASeq (RRID:SCR_000420) | software resource | Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. | software package, unix/linux, mac os x, windows, r, chip-seq, rna-seq, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23194258 | Free, Available for download, Freely available | OMICS_05505 | SCR_000420 | iASeq: integrating multiple sequencing datasets for detecting allele-specific events | 2026-09-05 06:24:19 | 0 | |||||||
|
PSCBS Resource Report Resource Website |
PSCBS (RRID:SCR_000417) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. | abnormal copy number regions detection, allele specific DNA copy number data segmentation, |
is listed by: OMICtools is listed by: Debian is related to: CRAN has parent organization: University of California at San Francisco; California; USA |
PMID:21666266 DOI:10.1093/bioinformatics/btr329 |
Free, Available for download, Freely available | OMICS_05545 | https://sources.debian.org/src/r-cran-pscbs/ | SCR_000417 | PSCBS: Analysis of Parent-Specific DNA Copy Numbers | 2026-09-05 06:24:19 | 0 | ||||||
|
rTANDEM Resource Report Resource Website |
rTANDEM (RRID:SCR_000409) | software resource | An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
is used by: shinyTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03516 | SCR_000409 | rTANDEM - Interfaces the tandem protein identification algorithm in R | 2026-09-05 06:24:19 | 0 | |||||||
|
NucleoFinder Resource Report Resource Website 1+ mentions |
NucleoFinder (RRID:SCR_000368) | NucleoFinder | software resource | A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes. | nucleusome, position, promoter, analysis, downstream, nucleotide, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23297036 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nucleofinder, OMICS_00510 | https://omictools.com/nucleofinder-tool, https://bio.tools/nucleofinder | SCR_000368 | 2026-09-05 06:24:18 | 1 | ||||||
|
flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-09-05 06:24:20 | 0 | |||||||
|
TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | 2026-09-05 06:24:19 | 0 | |||||||||
|
MiRdup Resource Report Resource Website 1+ mentions |
MiRdup (RRID:SCR_000316) | software resource | A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA. | pre-miRNA, miRNA, mRNA, splicing, predictions |
is listed by: OMICtools has parent organization: McGill University; Montreal; Canada |
PMID:23748953 | Free, Available for download, Freely available | OMICS_00404 | https://www.cs.mcgill.ca/~blanchem/mirdup/ | http://This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. | SCR_000316 | 2026-09-05 06:24:16 | 1 | ||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-09-05 06:24:18 | 0 | |||||||
|
rtd Resource Report Resource Website |
rtd (RRID:SCR_000337) | data analysis software, data processing software, software application, software resource | Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes. | standalone software | is listed by: OMICtools | PMID:22675423 | Free, Available for download, Freely available | OMICS_03723 | SCR_000337 | 2026-09-05 06:24:17 | 0 | ||||||||
|
oneClickCGH Resource Report Resource Website |
oneClickCGH (RRID:SCR_000294) | oneClickCGH | data analysis software, data processing software, software application, software resource | Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes. | array, comparative genomic hybridization, cytogenetics, copy number variant, copy number analysis, | is listed by: OMICtools | Restricted | OMICS_02050 | SCR_000294 | 2026-09-05 06:24:18 | 0 | ||||||||
|
fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | 2026-09-05 06:24:16 | 1 |
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